AMBER Archive (2009)

Subject: Re: [AMBER] Fail to allocate ff

From: Nicholas Musolino (musolino_at_MIT.EDU)
Date: Tue Mar 03 2009 - 07:10:21 CST

Hi Madhurima,

I believe that for estimating partial charges, parameters, etc.,
antechamber works for single ligands. If you include more than one
molecule in the MOL2 file, antechamber will be confused.

I think one approach that may work is to run antechamber with a single
CCL4 molecule, to get these parameters, and then create a system of
900 of them in tLeap. Think of it this way: you want partial charges
and parameters for CCL4 _as a species_, and then you might happen to
decide to simulate 900 of them, or 901 molecules, etc., later.

Nicholas

On Mar 3, 2009, at 6:17 AM, Madhurima Jana wrote:

> Hi All,
>
> I want to perform a MD simulation of CCL4 box using AMBER force field.
> For that I want to create the corresponding inpcrd and parmtop files.
> Actually my system contains 900 CCL4 molecule in an orthorhombic box.
> Using antechamber I was able to create a mol2 file for a single CCL4
> molecule and from that the corresponding inpcrd and parmtop files.
> But whenever I'm trying to do so for 900 molecules it is showing
> following error:
>
> The atom number exceeds the MAXATOM, reallocate memory
> Info: the bond number exceeds MAXBOND, reallocate memory automatically
>
> Info: the atom number exceeds the MAXATOM, reallocate memory
> automatically
> Total number of electrons: 66600; net charge: 0
>
> Running: $AMBERHOME/exe/divcon
> STOP Error: Fail to allocate ff
> Error: unable to find divcon charges in divcon.out
>
> Could anyone please suggest me how to overcome it.
>
> Thanks,
> Madhurima
>
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